Nieduszynski Conrad A, Hiraga Shin-ichiro, Ak Prashanth, Benham Craig J, Donaldson Anne D
Institute of Medical Science, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.
Nucleic Acids Res. 2007 Jan;35(Database issue):D40-6. doi: 10.1093/nar/gkl758. Epub 2006 Oct 25.
Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at www.oridb.org.
真核生物染色体的复制起始于多个被称为复制起点的位点。在芽殖酵母酿酒酵母中，对复制起点的理解最为透彻，多项互补研究已在全基因组范围内绘制出它们的位置。我们综合了这些数据集，同时考虑到每项研究的分辨率，生成了一份包含不同起点位点的单一列表。OriDB提供了一个基于网络的目录，用于收录这些已确认和预测的酿酒酵母DNA复制起点位点。每个提议的或已确认的起点位点在OriDB中都表现为一条记录，每条记录包含七个页面。这些页面以文本和图形格式提供以下信息：起点位点的基因组位置和染色体背景；起点复制时间；提议的或经实验确认的起点元件的DNA序列；打开DNA双链所需的自由能（应激诱导的DNA双链不稳定或SIDD）；以及序列元件的系统发育保守性。此外，OriDB鼓励社区通过“用户注释”功能为每个起点位点提交更多信息。起点位点与多个外部资源相关联，包括酿酒酵母基因组数据库（SGD）和PubMed上的相关出版物。最后，一个“染色体查看器”实用程序允许用户交互式地生成全基因组DNA复制数据的图形表示。可通过www.oridb.org访问OriDB。
